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Unverified Commit 182f7f15 authored by Andy Simmonett's avatar Andy Simmonett
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Nose-Hoover chain no longer derives from Force

parent ddaa3664
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Showing with 315 additions and 289 deletions
olla/include/openmm/kernels.h
View file @ 182f7f15
......@@ -1081,8 +1081,10 @@ public:
*
* @param context the context in which to execute this kernel
* @param integrator the VelocityVerletIntegrator this kernel is being used for
* @param forcesAreValid a reference to the parent integrator's boolean for keeping
* track of the validity of the current forces.
*/
virtual void execute(ContextImpl& context, const VelocityVerletIntegrator& integrator) = 0;
virtual void execute(ContextImpl& context, const VelocityVerletIntegrator& integrator, bool &forcesAreValid) = 0;
/**
* Compute the kinetic energy.
*
......
openmmapi/include/openmm/NoseHooverChain.h
View file @ 182f7f15
......@@ -51,20 +51,8 @@ namespace OpenMM {
* the number of MTS steps multiplied by the number of terms in the Yoshida-Suzuki decomposition.
*/
class OPENMM_EXPORT NoseHooverChain : public Force {
class OPENMM_EXPORT NoseHooverChain {
public:
/**
* This is the name of the parameter that stores the position of the ith bead
*/
std::string Position(int i) const {
return std::to_string(defaultChainID) + "NoseHooverChainPosition" + std::to_string(i);
}
/**
* This is the name of the parameter that stores the velocity of the ith bead
*/
std::string Velocity(int i) const {
return std::to_string(defaultChainID) + "NoseHooverChainVelocity" + std::to_string(i);
}
/**
* Create a NoseHooverChain.
*
......@@ -257,8 +245,6 @@ public:
bool usesPeriodicBoundaryConditions() const {
return false;
}
protected:
ForceImpl* createImpl() const;
private:
double defaultTemp, defaultFreq; //, defaultTimeStep;
int defaultNumDOFs, defaultChainLength, defaultNumMTS, defaultNumYS;
......
openmmapi/include/openmm/VelocityVerletIntegrator.h
View file @ 182f7f15
......@@ -136,6 +136,24 @@ public:
* associated with this integrator, at the current time.
*/
double computeHeatBathEnergy();
/**
* Get the number of Nose-Hoover chains registered with this integrator.
*/
int getNumNoseHooverChains() const {
return noseHooverChains.size();
}
/**
* This will be called by the Context when the user modifies aspects of the context state, such
* as positions, velocities, or parameters. This gives the Integrator a chance to discard cached
* information. This is <i>only</i> called when the user modifies information using methods of the Context
* object. It is <i>not</i> called when a ForceImpl object modifies state information in its updateContextState()
* method (unless the ForceImpl calls a Context method to perform the modification).
*
* @param changed this specifies what aspect of the Context was changed
*/
virtual void stateChanged(State::DataType changed) {
if (State::Positions == changed) forcesAreValid = false;
}
protected:
/**
......@@ -157,7 +175,8 @@ protected:
* Compute the kinetic energy of the system at the current time.
*/
double computeKineticEnergy();
std::map<int, NoseHooverChain*> noseHooverChains;
std::vector<NoseHooverChain> noseHooverChains;
bool forcesAreValid;
private:
Kernel vvKernel, nhcKernel;
};
......
openmmapi/include/openmm/internal/NoseHooverChainImpl.h deleted 100644 → 0
View file @ ddaa3664
#ifndef OPENMM_NOSEHOOVERCHAINIMPL_H_
#define OPENMM_NOSEHOOVERCHAINIMPL_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2019 Stanford University and the Authors. *
* Authors: Andreas Krämer and Andrew C. Simmonett *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "ForceImpl.h"
#include "openmm/NoseHooverChain.h"
#include "openmm/Kernel.h"
#include <string>
namespace OpenMM {
class System;
/**
* This is the internal implementation of NoseHooverChain.
*/
class OPENMM_EXPORT NoseHooverChainImpl : public ForceImpl {
public:
NoseHooverChainImpl(const NoseHooverChain& owner);
void initialize(ContextImpl& context);
const NoseHooverChain& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context, bool& forcesInvalid);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
std::map<std::string, double> getDefaultParameters();
std::vector<std::string> getKernelNames();
private:
const NoseHooverChain& owner;
};
} // namespace OpenMM
#endif /*OPENMM_NOSEHOOVERCHAINIMPL_H_*/
openmmapi/src/ContextImpl.cpp
View file @ 182f7f15
......@@ -486,6 +486,10 @@ void ContextImpl::loadCheckpoint(istream& stream) {
}
updateStateDataKernel.getAs<UpdateStateDataKernel>().loadCheckpoint(*this, stream);
hasSetPositions = true;
integrator.stateChanged(State::Positions);
integrator.stateChanged(State::Velocities);
integrator.stateChanged(State::Parameters);
integrator.stateChanged(State::Energy);
}
void ContextImpl::systemChanged() {
......
openmmapi/src/NoseHooverChain.cpp
View file @ 182f7f15
......@@ -30,7 +30,6 @@
* -------------------------------------------------------------------------- */
#include "openmm/NoseHooverChain.h"
#include "openmm/internal/NoseHooverChainImpl.h"
#include "openmm/OpenMMException.h"
using namespace OpenMM;
......@@ -44,9 +43,6 @@ NoseHooverChain::NoseHooverChain(double defaultTemperature, double defaultCollis
defaultChainID(defaultChainID), thermostatedAtoms(thermostatedAtoms), parentAtoms(parentAtoms)
{}
ForceImpl* NoseHooverChain::createImpl() const {
return new NoseHooverChainImpl(*this);
}
std::vector<double> NoseHooverChain::getDefaultYoshidaSuzukiWeights() const {
switch (defaultNumYS) {
......
openmmapi/src/NoseHooverChainImpl.cpp deleted 100644 → 0
View file @ ddaa3664
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2010 Stanford University and the Authors. *
* Authors: Andreas Krämer and Andrew C. Simmonett *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/NoseHooverChainImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/Integrator.h"
#include "openmm/System.h"
#include "openmm/kernels.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <string>
#include <vector>
#include <iostream>
using namespace OpenMM;
using std::vector;
NoseHooverChainImpl::NoseHooverChainImpl(const NoseHooverChain& owner) : owner(owner) {
}
void NoseHooverChainImpl::initialize(ContextImpl& context) {
}
void NoseHooverChainImpl::updateContextState(ContextImpl& context, bool& forcesInvalid) {
}
double NoseHooverChainImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
return 0;
}
std::map<std::string, double> NoseHooverChainImpl::getDefaultParameters() {
std::map<std::string, double> parameters;
const auto &owner = getOwner();
int chainLength = owner.getDefaultChainLength();
for(int i = 0; i < chainLength; ++i) {
parameters[owner.Position(i)] = 0;
parameters[owner.Velocity(i)] = 0;
}
return parameters;
}
std::vector<std::string> NoseHooverChainImpl::getKernelNames() {
return std::vector<std::string>();
}
openmmapi/src/VelocityVerletIntegrator.cpp
View file @ 182f7f15
......@@ -46,7 +46,9 @@ using namespace OpenMM;
using std::string;
using std::vector;
VelocityVerletIntegrator::VelocityVerletIntegrator(double stepSize) {
VelocityVerletIntegrator::VelocityVerletIntegrator(double stepSize):
forcesAreValid(false)
{
setStepSize(stepSize);
setConstraintTolerance(1e-5);
}
......@@ -54,7 +56,7 @@ VelocityVerletIntegrator::VelocityVerletIntegrator(double stepSize) {
VelocityVerletIntegrator::~VelocityVerletIntegrator() {}
double VelocityVerletIntegrator::propagateChain(double kineticEnergy, int chainID) {
return nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, *noseHooverChains.at(chainID), kineticEnergy, getStepSize());
return nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, noseHooverChains.at(chainID), kineticEnergy, getStepSize());
}
int VelocityVerletIntegrator::addNoseHooverChainThermostat(System& system, double temperature, double collisionFrequency,
......@@ -112,42 +114,25 @@ int VelocityVerletIntegrator::addMaskedNoseHooverChainThermostat(System& system,
}
}
// figure out the chain ID
std::vector<int> takenIDs;
for (int forceNum = 0; forceNum < numForces; ++forceNum){
const auto & other_nhc = dynamic_cast<NoseHooverChain*>(&system.getForce(forceNum));
if (other_nhc){
takenIDs.push_back(other_nhc->getDefaultChainID());
}
}
int chainID = 0;
while (true) {
bool isChainIDTaken = (std::find(takenIDs.begin(), takenIDs.end(), chainID) != takenIDs.end());
bool isChainIDRegistered = (noseHooverChains.find(chainID) != noseHooverChains.end());
if (isChainIDTaken || isChainIDRegistered) {
chainID ++;
} else {
break;
}
}
auto nhcForce = new NoseHooverChain(temperature, collisionFrequency, nDOF, chainLength,
numMTS, numYoshidaSuzuki, chainID,
thermostatedParticles, parentParticles);
// make sure that thermostats do not overlap
for (auto &other_nhc: noseHooverChains) {
for (auto &particle: mask){
bool isParticleInOtherChain = (std::find(other_nhc.second->getThermostatedAtoms().begin(),
other_nhc.second->getThermostatedAtoms().end(),
particle) == other_nhc.second->getThermostatedAtoms().begin());
bool isParticleInOtherChain = (std::find(other_nhc.getThermostatedAtoms().begin(),
other_nhc.getThermostatedAtoms().end(),
particle) == other_nhc.getThermostatedAtoms().begin());
if (isParticleInOtherChain){
throw OpenMMException("Found particle " + std::to_string(particle) + "in a different NoseHooverChain, "
"but particles can only be thermostated by one thermostat.");
}
}
}
system.addForce(nhcForce);
noseHooverChains[chainID] = nhcForce;
// create and add new chain
int chainID = noseHooverChains.size();
auto nhc = NoseHooverChain(temperature, collisionFrequency, nDOF, chainLength,
numMTS, numYoshidaSuzuki, chainID,
thermostatedParticles, parentParticles);
noseHooverChains.push_back(nhc);
return chainID;
}
......@@ -157,7 +142,7 @@ double VelocityVerletIntegrator::getTemperature(int chainID) const {
+ ". Only " + std::to_string(noseHooverChains.size()) + " have been registered with this integrator."
);
}
return noseHooverChains.at(chainID)->getDefaultTemperature();
return noseHooverChains.at(chainID).getDefaultTemperature();
}
void VelocityVerletIntegrator::setTemperature(double temperature, int chainID){
......@@ -166,7 +151,7 @@ void VelocityVerletIntegrator::setTemperature(double temperature, int chainID){
+ ". Only " + std::to_string(noseHooverChains.size()) + " have been registered with this integrator."
);
}
noseHooverChains.at(chainID)->setDefaultTemperature(temperature);
noseHooverChains.at(chainID).setDefaultTemperature(temperature);
}
......@@ -176,7 +161,7 @@ double VelocityVerletIntegrator::getCollisionFrequency(int chainID) const {
+ ". Only " + std::to_string(noseHooverChains.size()) + " have been registered with this integrator."
);
}
return noseHooverChains.at(chainID)->getDefaultCollisionFrequency();
return noseHooverChains.at(chainID).getDefaultCollisionFrequency();
}
void VelocityVerletIntegrator::setCollisionFrequency(double frequency, int chainID){
if (chainID >= noseHooverChains.size()) {
......@@ -184,7 +169,7 @@ void VelocityVerletIntegrator::setCollisionFrequency(double frequency, int chain
+ ". Only " + std::to_string(noseHooverChains.size()) + " have been registered with this integrator."
);
}
noseHooverChains.at(chainID)->setDefaultCollisionFrequency(frequency);
noseHooverChains.at(chainID).setDefaultCollisionFrequency(frequency);
}
double VelocityVerletIntegrator::computeKineticEnergy() {
......@@ -195,7 +180,7 @@ double VelocityVerletIntegrator::computeKineticEnergy() {
double VelocityVerletIntegrator::computeHeatBathEnergy() {
double energy = 0;
for(auto &nhc : noseHooverChains) {
energy += nhcKernel.getAs<NoseHooverChainKernel>().computeHeatBathEnergy(*context, *nhc.second);
energy += nhcKernel.getAs<NoseHooverChainKernel>().computeHeatBathEnergy(*context, nhc);
}
return energy;
}
......@@ -209,6 +194,7 @@ void VelocityVerletIntegrator::initialize(ContextImpl& contextRef) {
vvKernel.getAs<IntegrateVelocityVerletStepKernel>().initialize(contextRef.getSystem(), *this);
nhcKernel = context->getPlatform().createKernel(NoseHooverChainKernel::Name(), contextRef);
nhcKernel.getAs<NoseHooverChainKernel>().initialize();
forcesAreValid = false;
}
void VelocityVerletIntegrator::cleanup() {
......@@ -230,15 +216,15 @@ void VelocityVerletIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) {
context->updateContextState();
for(auto &nhc : noseHooverChains) {
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, *nhc.second);
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, *nhc.second, kineticEnergy, getStepSize());
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, *nhc.second, scale);
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, nhc);
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, nhc, kineticEnergy, getStepSize());
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, nhc, scale);
}
vvKernel.getAs<IntegrateVelocityVerletStepKernel>().execute(*context, *this);
vvKernel.getAs<IntegrateVelocityVerletStepKernel>().execute(*context, *this, forcesAreValid);
for(auto &nhc : noseHooverChains) {
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, *nhc.second);
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, *nhc.second, kineticEnergy, getStepSize());
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, *nhc.second, scale);
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, nhc);
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, nhc, kineticEnergy, getStepSize());
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, nhc, scale);
}
}
}
platforms/cuda/include/CudaArray.h
View file @ 182f7f15
......@@ -71,6 +71,10 @@ public:
* @param name the name of the array
*/
CudaArray(CudaContext& context, int size, int elementSize, const std::string& name);
CudaArray(const CudaArray &other) noexcept;
CudaArray& operator=(CudaArray &&other) noexcept;
CudaArray& operator=(const CudaArray& other) noexcept;
CudaArray(CudaArray &&other) noexcept ;
~CudaArray();
/**
* Initialize this object.
......
platforms/cuda/include/CudaKernels.h
View file @ 182f7f15
......@@ -1386,8 +1386,10 @@ public:
*
* @param context the context in which to execute this kernel
* @param integrator the VerletIntegrator this kernel is being used for
* @param forcesAreValid a reference to the parent integrator's boolean for keeping
* track of the validity of the current forces.
*/
void execute(ContextImpl& context, const VelocityVerletIntegrator& integrator);
void execute(ContextImpl& context, const VelocityVerletIntegrator& integrator, bool &forcesAreValid);
/**
* Compute the kinetic energy.
*
......
platforms/cuda/src/CudaArray.cpp
View file @ 182f7f15
......@@ -35,6 +35,47 @@ using namespace OpenMM;
CudaArray::CudaArray() : pointer(0), ownsMemory(false) {
}
CudaArray::CudaArray(const CudaArray &other) noexcept {
context = other.context;
pointer = other.pointer;
size = other.size;
elementSize = other.elementSize;
ownsMemory = false;
name = other.name;
}
CudaArray::CudaArray(CudaArray &&other) noexcept :
context(std::move(other.context)),
pointer(std::move(other.pointer)),
size(std::move(other.size)),
elementSize(std::move(other.elementSize)),
ownsMemory(false),
name(std::move(other.name)) { }
CudaArray& CudaArray::operator =(const CudaArray& other) noexcept{
if(this != &other) {
context = other.context;
pointer = other.pointer;
size = other.size;
elementSize = other.elementSize;
ownsMemory = false;
name = other.name;
}
return *this;
}
CudaArray& CudaArray::operator =(CudaArray &&other) noexcept{
if(this != &other) {
context = other.context;
pointer = other.pointer;
size = other.size;
elementSize = other.elementSize;
ownsMemory = false;
name = other.name;
}
return *this;
}
CudaArray::CudaArray(CudaContext& context, int size, int elementSize, const std::string& name) : pointer(0) {
initialize(context, size, elementSize, name);
}
......
platforms/cuda/src/CudaKernels.cpp
View file @ 182f7f15
......@@ -37,7 +37,6 @@
#include "openmm/internal/CustomManyParticleForceImpl.h"
#include "openmm/internal/CustomNonbondedForceImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "openmm/internal/NoseHooverChainImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "CudaBondedUtilities.h"
#include "CudaExpressionUtilities.h"
......@@ -7087,7 +7086,7 @@ void CudaIntegrateVelocityVerletStepKernel::initialize(const System& system, con
kernel3 = cu.getKernel(module, "integrateVelocityVerletPart3");
}
void CudaIntegrateVelocityVerletStepKernel::execute(ContextImpl& context, const VelocityVerletIntegrator& integrator) {
void CudaIntegrateVelocityVerletStepKernel::execute(ContextImpl& context, const VelocityVerletIntegrator& integrator, bool &forcesAreValid) {
cu.setAsCurrent();
CudaIntegrationUtilities& integration = cu.getIntegrationUtilities();
int numAtoms = cu.getNumAtoms();
......@@ -7095,6 +7094,8 @@ void CudaIntegrateVelocityVerletStepKernel::execute(ContextImpl& context, const
double dt = integrator.getStepSize();
cu.getIntegrationUtilities().setNextStepSize(dt);
if( !forcesAreValid ) context.calcForcesAndEnergy(true, false);
//// Call the first integration kernel.
CUdeviceptr posCorrection = (cu.getUseMixedPrecision() ? cu.getPosqCorrection().getDevicePointer() : 0);
......@@ -7116,6 +7117,7 @@ void CudaIntegrateVelocityVerletStepKernel::execute(ContextImpl& context, const
//// Update forces
context.calcForcesAndEnergy(true, false);
forcesAreValid = true;
//// Call the third integration kernel.
......@@ -8390,16 +8392,16 @@ double CudaNoseHooverChainKernel::propagateChain(ContextImpl& context, const Nos
auto & chainState = cu.getIntegrationUtilities().getNoseHooverChainState();
if (chainID >= chainState.size()) chainState.resize(chainID+1);
if (!chainState[chainID].isInitialized() || chainState[chainID].getSize() != chainLength) {
if (!chainState.at(chainID).isInitialized() || chainState.at(chainID).getSize() != chainLength) {
// We need to upload the CUDA array
if(useDouble){
chainState[chainID].initialize<double2>(cu, chainLength, "chainState" + std::to_string(chainID));
chainState.at(chainID).initialize<double2>(cu, chainLength, "chainState" + std::to_string(chainID));
std::vector<double2> zeros(chainLength, make_double2(0, 0));
chainState[chainID].upload(zeros.data());
chainState.at(chainID).upload(zeros.data());
} else {
chainState[chainID].initialize<float2>(cu, chainLength, "chainState" + std::to_string(chainID));
chainState.at(chainID).initialize<float2>(cu, chainLength, "chainState" + std::to_string(chainID));
std::vector<float2> zeros(chainLength, make_float2(0, 0));
chainState[chainID].upload(zeros.data());
chainState.at(chainID).upload(zeros.data());
}
}
......@@ -8415,21 +8417,22 @@ double CudaNoseHooverChainKernel::propagateChain(ContextImpl& context, const Nos
}
}
if (!chainForces.isInitialized() || !chainMasses.isInitialized() || chainForces.getSize() < chainLength || chainMasses.getSize() < chainLength) {
std::vector<double> zeros(chainLength,0);
if (!chainForces.isInitialized() || !chainMasses.isInitialized() ){
if(useDouble){
std::vector<double> zeros(chainLength,0);
chainMasses.initialize<double>(cu, chainLength, "chainMasses");
chainForces.initialize<double>(cu, chainLength, "chainForces");
chainMasses.upload(zeros);
chainForces.upload(zeros);
} else {
std::vector<float> zeros(chainLength,0);
chainMasses.initialize<float>(cu, chainLength, "chainMasses");
chainForces.initialize<float>(cu, chainLength, "chainForces");
chainMasses.upload(zeros);
chainForces.upload(zeros);
}
}
if (chainForces.getSize() < chainLength) chainMasses.resize(chainLength);
if (chainMasses.getSize() < chainLength) chainMasses.resize(chainLength);
double kT = BOLTZ * temperature;
float kTfloat = (float) kT;
float timeStepFloat = (float) timeStep;
......@@ -8511,7 +8514,7 @@ double CudaNoseHooverChainKernel::computeMaskedKineticEnergy(ContextImpl& contex
const auto & thermostatedAtoms = nhc.getThermostatedAtoms();
if (chainID >= masks.size()) masks.resize(chainID+1);
auto nAtoms = cu.getPaddedNumAtoms();
if (!masks[chainID].isInitialized()) {
if (!masks.at(chainID).isInitialized()) {
// We need to upload the CUDA array
std::vector<int> maskVec(nAtoms);
for (int i = 0; i < nAtoms; ++i) maskVec[i] = i;
......@@ -8531,8 +8534,8 @@ double CudaNoseHooverChainKernel::computeMaskedKineticEnergy(ContextImpl& contex
for(int i = thermostatedAtoms.size(); i < nAtoms; ++i){
maskVec[i] = i;
}
masks[chainID].initialize<int>(cu, nAtoms, "mask" + std::to_string(chainID));
masks[chainID].upload(maskVec);
masks.at(chainID).initialize<int>(cu, nAtoms, "mask" + std::to_string(chainID));
masks.at(chainID).upload(maskVec);
}
if (masks[chainID].getSize() != nAtoms) {
throw OpenMMException("Number of atoms changed. Cannot be handled by the same Nose-Hoover thermostat.");
......
platforms/reference/include/ReferenceKernels.h
View file @ 182f7f15
......@@ -1156,8 +1156,10 @@ public:
*
* @param context the context in which to execute this kernel
* @param integrator the VerletIntegrator this kernel is being used for
* @param forcesAreValid a reference to the parent integrator's boolean for keeping
* track of the validity of the current forces.
*/
void execute(ContextImpl& context, const VelocityVerletIntegrator& integrator);
void execute(ContextImpl& context, const VelocityVerletIntegrator& integrator, bool &forcesAreValid);
/**
* Compute the kinetic energy.
*
......
platforms/reference/include/ReferencePlatform.h
View file @ 182f7f15
......@@ -72,6 +72,8 @@ public:
Vec3* periodicBoxVectors;
ReferenceConstraints* constraints;
std::map<std::string, double>* energyParameterDerivatives;
std::vector<std::vector<double>>* noseHooverPositions;
std::vector<std::vector<double>>* noseHooverVelocities;
};
} // namespace OpenMM
......
platforms/reference/include/ReferenceVelocityVerletDynamics.h
View file @ 182f7f15
......@@ -70,11 +70,12 @@ class ReferenceVelocityVerletDynamics : public ReferenceDynamics {
@param forces forces
@param masses atom masses
@param tolerance the constraint tolerance
@param forcesAreValid whether the forces are valid (duh!)
--------------------------------------------------------------------------------------- */
void update(OpenMM::ContextImpl &context, const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double tolerance);
std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double tolerance, bool &forcesAreValid);
};
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 182f7f15
......@@ -126,6 +126,15 @@ static map<string, double>& extractEnergyParameterDerivatives(ContextImpl& conte
return *data->energyParameterDerivatives;
}
static vector<vector<double> >& extractNoseHooverPositions(ContextImpl& context) {
ReferencePlatform::PlatformData *data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *((vector<vector<double> >*) data->noseHooverPositions);
}
static vector<vector<double> >& extractNoseHooverVelocities(ContextImpl& context) {
ReferencePlatform::PlatformData *data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *((vector<vector<double> >*) data->noseHooverVelocities);
}
/**
* Make sure an expression doesn't use any undefined variables.
*/
......@@ -278,7 +287,7 @@ void ReferenceUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context,
}
void ReferenceUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream& stream) {
int version = 2;
int version = 3;
stream.write((char*) &version, sizeof(int));
stream.write((char*) &data.time, sizeof(data.time));
vector<Vec3>& posData = extractPositions(context);
......@@ -287,13 +296,27 @@ void ReferenceUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostr
stream.write((char*) &velData[0], sizeof(Vec3)*velData.size());
Vec3* vectors = extractBoxVectors(context);
stream.write((char*) vectors, 3*sizeof(Vec3));
auto& allNoseHooverPositions = extractNoseHooverPositions(context);
auto& allNoseHooverVelocities = extractNoseHooverVelocities(context);
size_t numChains = allNoseHooverPositions.size();
assert(numChains == allNoseHooverVelocities.size());
stream.write((char*) &numChains, sizeof(size_t));
for (size_t i=0; i<numChains; i++){
auto & noseHooverPositions = allNoseHooverPositions.at(i);
auto & noseHooverVelocities = allNoseHooverVelocities.at(i);
size_t numBeads = noseHooverPositions.size();
assert(numBeads == noseHooverVelocities.size());
stream.write((char*) &numBeads, sizeof(size_t));
stream.write((char*) noseHooverPositions.data(), sizeof(double)*numBeads);
stream.write((char*) noseHooverVelocities.data(), sizeof(double)*numBeads);
}
SimTKOpenMMUtilities::createCheckpoint(stream);
}
void ReferenceUpdateStateDataKernel::loadCheckpoint(ContextImpl& context, istream& stream) {
int version;
stream.read((char*) &version, sizeof(int));
if (version != 2)
if (version != 3)
throw OpenMMException("Checkpoint was created with a different version of OpenMM");
stream.read((char*) &data.time, sizeof(data.time));
vector<Vec3>& posData = extractPositions(context);
......@@ -302,6 +325,21 @@ void ReferenceUpdateStateDataKernel::loadCheckpoint(ContextImpl& context, istrea
stream.read((char*) &velData[0], sizeof(Vec3)*velData.size());
Vec3* vectors = extractBoxVectors(context);
stream.read((char*) vectors, 3*sizeof(Vec3));
size_t numChains, numBeads;
auto& allNoseHooverPositions = extractNoseHooverPositions(context);
auto& allNoseHooverVelocities = extractNoseHooverVelocities(context);
stream.read((char*) &numChains, sizeof(size_t));
allNoseHooverPositions.clear();
allNoseHooverVelocities.clear();
for (size_t i=0; i<numChains; i++){
stream.read((char*) &numBeads, sizeof(size_t));
std::vector<double> noseHooverPositions(numBeads);
std::vector<double> noseHooverVelocities(numBeads);
stream.read((char*) &noseHooverPositions[0], sizeof(double)*numBeads);
stream.read((char*) &noseHooverVelocities[0], sizeof(double)*numBeads);
allNoseHooverPositions.push_back(noseHooverPositions);
allNoseHooverVelocities.push_back(noseHooverVelocities);
}
SimTKOpenMMUtilities::loadCheckpoint(stream);
}
......@@ -2119,7 +2157,7 @@ void ReferenceIntegrateVelocityVerletStepKernel::initialize(const System& system
masses[i] = system.getParticleMass(i);
}
void ReferenceIntegrateVelocityVerletStepKernel::execute(ContextImpl& context, const VelocityVerletIntegrator& integrator) {
void ReferenceIntegrateVelocityVerletStepKernel::execute(ContextImpl& context, const VelocityVerletIntegrator& integrator, bool &forcesAreValid) {
double stepSize = integrator.getStepSize();
vector<Vec3>& posData = extractPositions(context);
vector<Vec3>& velData = extractVelocities(context);
......@@ -2132,7 +2170,7 @@ void ReferenceIntegrateVelocityVerletStepKernel::execute(ContextImpl& context, c
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
prevStepSize = stepSize;
}
dynamics->update(context, context.getSystem(), posData, velData, forceData, masses, integrator.getConstraintTolerance());
dynamics->update(context, context.getSystem(), posData, velData, forceData, masses, integrator.getConstraintTolerance(), forcesAreValid);
data.time += stepSize;
data.stepCount++;
}
......@@ -2436,27 +2474,32 @@ double ReferenceNoseHooverChainKernel::propagateChain(ContextImpl& context, cons
if (kineticEnergy < 1e-8) return 1.0; // (catches the problem of zero velocities in the first dynamics step, where we have nothing to scale)
// Get the variables describing the NHC
int chainLength = nhc.getDefaultChainLength();
int chainID = nhc.getDefaultChainID();
double temperature = nhc.getDefaultTemperature();
double collisionFrequency = nhc.getDefaultCollisionFrequency();
int numDOFs = nhc.getDefaultNumDegreesOfFreedom();
int numMTS = nhc.getDefaultNumMultiTimeSteps();
// Get the state of the NHC from the context
std::vector<double> chainPositions(chainLength), chainVelocities(chainLength);
for(int i = 0; i < chainLength; ++i) {
chainPositions[i] = context.getParameter(nhc.Position(i));
chainVelocities[i] = context.getParameter(nhc.Velocity(i));
auto& allChainPositions = extractNoseHooverPositions(context);
auto& allChainVelocities = extractNoseHooverVelocities(context);
if (allChainPositions.size() < chainID+1){
allChainPositions.resize(chainID+1);
}
if (allChainVelocities.size() < chainID+1){
allChainVelocities.resize(chainID+1);
}
auto& chainPositions = allChainPositions.at(chainID);
auto& chainVelocities = allChainVelocities.at(chainID);
if (chainPositions.size() < chainLength){
chainPositions.resize(chainLength, 0);
}
if (chainVelocities.size() < chainLength){
chainVelocities.resize(chainLength, 0);
}
double scale = chainPropagator->propagate(kineticEnergy, chainVelocities, chainPositions, numDOFs,
temperature, collisionFrequency, timeStep,
numMTS, nhc.getDefaultYoshidaSuzukiWeights());
// Update the state of the NHC in the context
for(int i = 0; i < chainLength; ++i) {
context.setParameter(nhc.Position(i), chainPositions[i]);
context.setParameter(nhc.Velocity(i), chainVelocities[i]);
}
return scale;
}
......@@ -2464,18 +2507,21 @@ double ReferenceNoseHooverChainKernel::computeHeatBathEnergy(ContextImpl& contex
double potentialEnergy = 0;
double kineticEnergy = 0;
int chainLength = nhc.getDefaultChainLength();
int chainID = nhc.getDefaultChainID();
double temperature = nhc.getDefaultTemperature();
double collisionFrequency = nhc.getDefaultCollisionFrequency();
double kT = temperature * BOLTZ;
int numDOFs = nhc.getDefaultNumDegreesOfFreedom();
auto& nhcPositions = extractNoseHooverPositions(context);
auto& nhcVelocities = extractNoseHooverVelocities(context);
for(int i = 0; i < chainLength; ++i) {
double prefac = i ? 1 : numDOFs;
double mass = prefac * kT / (collisionFrequency * collisionFrequency);
double velocity = context.getParameter(nhc.Velocity(i));
double velocity = nhcVelocities[chainID][i];
// The kinetic energy of this bead
kineticEnergy += 0.5 * mass * velocity * velocity;
// The potential energy of this bead
double position = context.getParameter(nhc.Position(i));
double position = nhcPositions[chainID][i];
potentialEnergy += prefac * kT * position;
}
return kineticEnergy + potentialEnergy;
......@@ -2485,7 +2531,6 @@ double ReferenceNoseHooverChainKernel::computeMaskedKineticEnergy(ContextImpl& c
const std::vector<int>& mask = noseHooverChain.getThermostatedAtoms();
const std::vector<int>& parents = noseHooverChain.getParentAtoms();
std::vector<Vec3>& velocities = extractVelocities(context);
// TODO move these bad boys into the class
const System& system = context.getSystem();
int numParticles = system.getNumParticles();
std::vector<double> masses(numParticles);
......
platforms/reference/src/ReferencePlatform.cpp
View file @ 182f7f15
......@@ -103,6 +103,8 @@ ReferencePlatform::PlatformData::PlatformData(const System& system) : time(0.0),
periodicBoxVectors = new Vec3[3];
constraints = new ReferenceConstraints(system);
energyParameterDerivatives = new map<string, double>();
noseHooverPositions = new vector<vector<double> >();
noseHooverVelocities = new vector<vector<double> >();
}
ReferencePlatform::PlatformData::~PlatformData() {
......@@ -113,4 +115,6 @@ ReferencePlatform::PlatformData::~PlatformData() {
delete[] periodicBoxVectors;
delete constraints;
delete energyParameterDerivatives;
delete noseHooverPositions;
delete noseHooverVelocities;
}
platforms/reference/src/SimTKReference/ReferenceNoseHooverChain.cpp
View file @ 182f7f15
......@@ -26,7 +26,6 @@
#include <string.h>
#include <sstream>
#include <exception>
#include <iostream>
#include "SimTKOpenMMUtilities.h"
#include "ReferenceNoseHooverChain.h"
......
platforms/reference/src/SimTKReference/ReferenceVelocityVerletDynamics.cpp
View file @ 182f7f15
......@@ -77,59 +77,61 @@ ReferenceVelocityVerletDynamics::~ReferenceVelocityVerletDynamics() {
void ReferenceVelocityVerletDynamics::update(OpenMM::ContextImpl &context, const OpenMM::System& system, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& masses, double tolerance) {
// first-time-through initialization
int numberOfAtoms = system.getNumParticles();
if (getTimeStep() == 0) {
// invert masses
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == 0.0)
inverseMasses[ii] = 0.0;
else
inverseMasses[ii] = 1.0/masses[ii];
}
}
// Perform the integration.
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
velocities[i][j] += 0.5 * inverseMasses[i]*forces[i][j]*getDeltaT();
xPrime[i][j] = atomCoordinates[i][j];
atomCoordinates[i][j] += velocities[i][j]*getDeltaT();
}
}
//
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(xPrime, atomCoordinates, inverseMasses, tolerance);
ReferenceVirtualSites::computePositions(system, atomCoordinates);
context.calcForcesAndEnergy(true, false);
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
xPrime[i][j] += velocities[i][j]*getDeltaT();
}
}
// Update the positions and velocities.
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
velocities[i][j] += 0.5*inverseMasses[i]*forces[i][j]*getDeltaT() + (atomCoordinates[i][j] - xPrime[i][j]) / getDeltaT();
}
}
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
incrementTimeStep();
vector<Vec3>& forces, vector<double>& masses, double tolerance, bool &forcesAreValid) {
// first-time-through initialization
if (!forcesAreValid) context.calcForcesAndEnergy(true, false);
int numberOfAtoms = system.getNumParticles();
if (getTimeStep() == 0) {
// invert masses
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == 0.0)
inverseMasses[ii] = 0.0;
else
inverseMasses[ii] = 1.0/masses[ii];
}
}
// Perform the integration.
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
velocities[i][j] += 0.5 * inverseMasses[i]*forces[i][j]*getDeltaT();
xPrime[i][j] = atomCoordinates[i][j];
atomCoordinates[i][j] += velocities[i][j]*getDeltaT();
}
}
//
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(xPrime, atomCoordinates, inverseMasses, tolerance);
ReferenceVirtualSites::computePositions(system, atomCoordinates);
context.calcForcesAndEnergy(true, false);
forcesAreValid = true;
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
xPrime[i][j] += velocities[i][j]*getDeltaT();
}
}
// Update the positions and velocities.
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
velocities[i][j] += 0.5*inverseMasses[i]*forces[i][j]*getDeltaT() + (atomCoordinates[i][j] - xPrime[i][j]) / getDeltaT();
}
}
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
incrementTimeStep();
}
tests/TestNoseHooverThermostat.h
View file @ 182f7f15
......@@ -33,6 +33,7 @@
#include "openmm/NoseHooverChain.h"
#include "openmm/VelocityVerletIntegrator.h"
#include "openmm/Context.h"
#include "openmm/State.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/CustomExternalForce.h"
......@@ -40,9 +41,11 @@
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <sstream>
#include <iomanip>
#include <vector>
#include <algorithm>
#include <numeric>
using namespace OpenMM;
using namespace std;
......@@ -260,6 +263,67 @@ void testPropagateChainConsistentWithPythonReference() {
ASSERT_EQUAL_TOL(0.9674732261005896, scale, 1e-5)
}
void testCheckpoints() {
VelocityVerletIntegrator integrator(0.001);
System system;
double mass = 1;
system.addParticle(mass);
system.addParticle(mass);
NonbondedForce* force = new NonbondedForce();
force->addParticle(0, 0.1, 1.0);
force->addParticle(0, 0.1, 1.0);
system.addForce(force);
double kineticEnergy = 1e6;
double temperature=300, collisionFrequency=1, chainLength=3, numMTS=3, numYS=3;
integrator.addMaskedNoseHooverChainThermostat(system, std::vector<int>(1,0), std::vector<int>(), temperature, collisionFrequency,
chainLength, numMTS, numYS);
chainLength = 10;
integrator.addMaskedNoseHooverChainThermostat(system, std::vector<int>(1,1), std::vector<int>(1,0),
temperature, collisionFrequency,
chainLength, numMTS, numYS);
Context context(system, integrator, platform);
std::vector<Vec3> positions(2);
positions[1] = {0.1,0.1,0.1};
context.setPositions(positions);
integrator.step(300);
#if DEBUG
std::cout << std::endl << std::endl << std::endl << "writing checkpoint";
#endif
std::stringstream checkpoint;
context.createCheckpoint(checkpoint);
State state = context.getState(State::Positions | State::Velocities);
for (size_t i=0; i<100; i++){
state = context.getState(State::Positions | State::Velocities);
#if DEBUG
std::cout << "posvel" << state.getPositions()[0] << " " << state.getVelocities()[0] << std::endl;
#endif
integrator.step(1);
}
#if DEBUG
std::cout << std::endl << std::endl << "loading checkpoint" << std::endl;
#endif
context.loadCheckpoint(checkpoint);
State state2 = context.getState(State::Positions | State::Velocities);
for (size_t i=0; i<100; i++){
state2 = context.getState(State::Positions | State::Velocities);
#if DEBUG
std::cout << "posvel" << state2.getPositions()[0] << " " << state2.getVelocities()[0] << std::endl;
#endif
integrator.step(1);
}
for (int i=0; i<3;i++){
ASSERT_EQUAL_VEC(state.getPositions()[0], state2.getPositions()[0], 1e-6);
ASSERT_EQUAL_VEC(state.getPositions()[1], state2.getPositions()[1], 1e-6);
ASSERT_EQUAL_VEC(state.getVelocities()[0], state2.getVelocities()[0], 1e-6);
ASSERT_EQUAL_VEC(state.getVelocities()[1], state2.getVelocities()[1], 1e-6);
}
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -269,6 +333,7 @@ int main(int argc, char* argv[]) {
bool constrain;
constrain = false; testDimerBox(constrain);
constrain = true; testDimerBox(constrain);
testCheckpoints();
runPlatformTests();
}
catch(const exception& e) {
......
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